Mercurial > repos > devteam > snpeff_with_dep
view snpeff_with_dep-244c09911d7a/snpSift_caseControl.xml @ 1:515163fbe70f draft
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author | devteam |
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date | Thu, 27 Sep 2012 14:10:46 -0400 |
parents | d8bd4326dc3a |
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<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="1.0"> <description>Count samples are in 'case' and 'control' groups.</description> <!-- You will need to change the path to wherever your installation is. You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) --> <requirements> <requirement type="package" version="1.7">SnpSift</requirement> </requirements> <command> java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output </command> <inputs> <param format="vcf" name="input" type="data" label="VCF input"/> <param name="hhCase" type="select" label="Hom/Het case"> <option value="any">Any</option> <option value="hom">Homozygous</option> <option value="het">Heterozygous</option> </param> <param name="hhControl" type="select" label="Hom/Het control"> <option value="any">Any</option> <option value="hom">Homozygous</option> <option value="het">Heterozygous</option> </param> <param name="caseControStr" type="text" label="Case / Control" size="50"/> </inputs> <outputs> <data format="vcf" name="output" /> </outputs> <stdio> <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> <exit_code range="1:" level="fatal" description="Error" /> </stdio> <help> Count samples are in 'case' and 'control' groups. You can count 'homozygous', 'heterozygous' or 'any' variants. Case and control are defined by a string containing plus and minus symbols ('+' and '-') where '+' is case and '-' is control. This command adds two annotations to the VCF file. For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol </help> </tool>